Abstract Detail

Effects of substitution models on divergence time estimates: an empirical study of model uncertainty using Cornales.

The rate of phylogenetic divergence over time, whether based on a relaxed or strict molecular clock, is estimated with branch length data. Thus, the ages of clades are directly influenced by branch lengths estimated by phylogenetic inference. Furthermore, during phylogenetic inference with maximum likelihood optimization, the estimates of branch lengths are dependent upon the substitution model. We explored the effects of alternative substitution models on branch lengths and absolute divergence time estimates using an empirical data set for Cornales that applied 16 calibration point constraints. Maximum likelihood analyses were conducted using 19 different substitution models to obtain topologies with branch lengths, and these trees were subjected to penalized likelihood analyses to compare divergence time estimates for corresponding nodes. Variation in divergence time estimates among corresponding nodes of trees constructed with different models was small (falling within 95% confidence intervals based on our best estimates) in most cases; however, we recovered instances of nodes varying as much as 23.7% from times on corresponding nodes of the topology reconstructed from our best-fit substitution model. We estimated that, on average for all nodes within a tree, alternative substitution models vary 1.0--3.6% in divergence time estimates from those for the tree based on our best-fit model. Disproportionately more variation of divergence time estimates was associated with long branches and a constant amount of low variation was associated with shorter branches. Shallow nodes had greater variation in divergence time estimates than mid- or deep-level nodes of the tree. This contrasts with results of earlier studies of model misspecification that have pointed to branches deep in trees as being disproportionately influenced by substitution models.